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- PDB-9ovt: Heteromeric GluA1/A2 in the inactive state, composite map of LBD-TMD -

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Basic information

Entry
Database: PDB / ID: 9ovt
TitleHeteromeric GluA1/A2 in the inactive state, composite map of LBD-TMD
Components
  • Glutamate receptor 1
  • Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / GluA1A2 heterotetramer ZK iGluR
Function / homology
Function and homology information


Cargo concentration in the ER / axonal spine / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / COPII-mediated vesicle transport / cellular response to ammonium ion / response to sucrose / myosin V binding / neuron spine / proximal dendrite ...Cargo concentration in the ER / axonal spine / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / COPII-mediated vesicle transport / cellular response to ammonium ion / response to sucrose / myosin V binding / neuron spine / proximal dendrite / Trafficking of AMPA receptors / response to arsenic-containing substance / regulation of monoatomic ion transmembrane transport / cellular response to L-glutamate / cellular response to dsRNA / ligand-gated calcium channel activity / dendritic spine membrane / beta-2 adrenergic receptor binding / Synaptic adhesion-like molecules / long-term synaptic depression / cellular response to peptide hormone stimulus / spine synapse / dendritic spine neck / dendritic spine cytoplasm / cellular response to amine stimulus / dendritic spine head / response to psychosocial stress / peptide hormone receptor binding / response to morphine / Activation of AMPA receptors / spinal cord development / ligand-gated monoatomic cation channel activity / perisynaptic space / neuronal cell body membrane / protein kinase A binding / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / AMPA glutamate receptor clustering / behavioral response to pain / kainate selective glutamate receptor activity / immunoglobulin binding / adenylate cyclase binding / asymmetric synapse / AMPA glutamate receptor complex / response to electrical stimulus / regulation of receptor recycling / extracellularly glutamate-gated ion channel activity / cellular response to glycine / ionotropic glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / G-protein alpha-subunit binding / glutamate receptor binding / conditioned place preference / positive regulation of synaptic transmission / long-term memory / postsynaptic density, intracellular component / response to fungicide / neuronal action potential / regulation of synaptic transmission, glutamatergic / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / cytoskeletal protein binding / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / somatodendritic compartment / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / synapse assembly / excitatory synapse / ionotropic glutamate receptor signaling pathway / ionotropic glutamate receptor binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / positive regulation of excitatory postsynaptic potential / dendritic shaft / SNARE binding / synaptic membrane / response to cocaine / PDZ domain binding / neuromuscular junction / cellular response to amino acid stimulus / establishment of protein localization / synaptic transmission, glutamatergic / protein tetramerization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to nutrient levels / cerebral cortex development / regulation of synaptic plasticity / receptor internalization / recycling endosome / postsynaptic density membrane / response to peptide hormone / cellular response to growth factor stimulus / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / response to toxic substance / small GTPase binding / recycling endosome membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Chem-ZK1 / Glutamate receptor 1 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsYen, L.Y. / Sobolevsky, A.I. / Newton, T.P. / Gangwar, S.P.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129539 United States
Simons FoundationSF349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129541 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F31NS132554 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS139087 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS083660 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS107253 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR078814 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA206573 United States
CitationJournal: Nat Commun / Year: 2026
Title: Auxiliary subunits reshape structural asymmetry and functional plasticity in heterotetrameric GluA1/A2 AMPA receptor core.
Authors: Laura Y Yen / Thomas P Newton / Maria V Yelshanskaya / Muhammed Aktolun / Shanti Pal Gangwar / Rasmus P Clausen / Maria G Kurnikova / Alexander I Sobolevsky /
Abstract: AMPA-subtype ionotropic glutamate receptors (AMPARs) mediate the fast component of excitatory neurotransmission. They govern synaptic plasticity that underlies learning and memory, while their ...AMPA-subtype ionotropic glutamate receptors (AMPARs) mediate the fast component of excitatory neurotransmission. They govern synaptic plasticity that underlies learning and memory, while their dysregulation is implicated in numerous neurological disorders. The functional diversity of AMPARs arises from variations in their subunit composition and also their association with auxiliary subunits. While multiple structures of homomeric AMPARs have been reported, structural information for the heteromeric core - particularly in the absence of auxiliary subunits, which would serve as a functional and structural baseline - has been limited. Here, we report cryo-electron microscopy structures of GluA1/A2, the most abundant AMPAR di-heteromer in the brain, in the closed, open, and desensitized states. Using molecular dynamics (MD) simulations and cross-correlating structural and functional information, we find that auxiliary subunits increase the diameter of channel pore, which corresponds to larger conductance. Likewise, we find that recovery from desensitization slows with greater disruption of two-fold rotational symmetry of the ligand-binding domain dimer in the desensitized state. Both receptor activation and desensitization vary with the type and number of associated auxiliary proteins. These structures offer a foundation for uncovering how auxiliary subunits reshape structural asymmetry and functional plasticity in heterotetrameric AMPARs.
History
DepositionMay 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 1
B: Glutamate receptor 2
C: Glutamate receptor 1
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,57611
Polymers191,8704
Non-polymers1,7067
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Glutamate receptor 1 / GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / AMPA 1


Mass: 48183.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria1, GluA1, Glur1 / Plasmid: pEG BacMam / Cell (production host): epithelial / Cell line (production host): HEK 293S GntI- / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): kidney / References: UniProt: P19490
#2: Protein Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2


Mass: 47751.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, GluA2, Glur2 / Plasmid: pEG BacMam / Cell (production host): epithelial / Cell line (production host): HEK 293S GntI- / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): kidney / References: UniProt: P19491
#3: Chemical
ChemComp-ZK1 / {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / [[3,4-Dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluorom ethyl)-1(2H)-quinoxalinyl]methyl]phosphonic acid


Mass: 409.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15F3N3O6P / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist, medication*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Heteromeric GluA1A2 with competitive antagonist ZK / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.556 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK 293S GntI- / Plasmid: pEG BacMam
Buffer solutionpH: 8
Details: 150 mM NaCl, 20 mM Tris-HCl pH 8.0, and 0.05% digitonin, 100 uM ZK-200775
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMTris-HCl (pH 8.0)C4H11NO31
30.05 %digitoninC56H92O291
4100 uMZK-200775C14H15N3O6F3P1
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample had compositional heterogeneity, with broken particles seen throughout. Otherwise, sample was monodisperse
Specimen supportDetails: 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 45.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.11.1_2575model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5527903
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 216104
Details: this is a composite map; where required, consensus refinement parameters are entered
Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413298
ELECTRON MICROSCOPYf_angle_d1.04717972
ELECTRON MICROSCOPYf_dihedral_angle_d10.4647832
ELECTRON MICROSCOPYf_chiral_restr0.0511962
ELECTRON MICROSCOPYf_plane_restr0.0072218

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